Structure, Charge and Spin Density in Na2Ni(CN)4.3H2O at 295 and 30 K

1998 ◽  
Vol 54 (5) ◽  
pp. 600-612 ◽  
Author(s):  
H. Ptasiewicz-Bak ◽  
I. Olovsson ◽  
G. J. McIntyre
Keyword(s):  
Neutron Diffraction ◽  
Crystal Field ◽  
Spin Density ◽  
Lone Pair ◽  
Water Molecules ◽  
Sodium Ions ◽  
X Ray Diffraction ◽  
X Ray ◽  
Deformation Density ◽  
The Individual

The earlier reported structure of the title compound, disodium tetracyanonickelate(II) trihydrate, Na2Ni(CN)4.3H2O, has been found to be incorrect and has now been redetermined. The charge distribution has been determined by multipole refinements against single-crystal X-ray diffraction data. In the refinement based on 30 K data a comparison was made between the results obtained using hydrogen positions and displacement parameters from X-ray diffraction with those using the values determined by neutron diffraction. The spin density was investigated by polarized neutron diffraction at 1.6 K. Crystal data: at T = 30 K: a = 7.278 (4), b = 8.856 (5), c = 15.131 (8) Å, α = 89.32 (5), β = 87.39 (4), γ = 83.61 (4)°; at 295 K: a = 7.392 (4), b = 8.895 (4), c = 15.115 (8)  Å, α = 89.12 (2), β = 87.46 (2), γ = 84.54 (2)°. The structure contains practically square planar Ni(CN)_4^{2-} ions, which are stacked on top of each other in almost linear chains along the a direction. The separation between the Ni(CN)_4^{2-} planes is rather large, with Ni—Ni distances around 3.7 Å. The six crystallographically independent water molecules are each coordinated to two sodium ions, approximately in the tetrahedral (lone-pair) directions, and the polarizing influence of these sodium ions also appears to be reflected in the deformation density in the lone-pair plane. The charge density based on the deformation functions of all atoms in the structure is compared with the individual densities calculated from the deformation functions of only nickel or the separate water molecules. In this way the effects of simple superposition of the individual densities have been studied. In the planar Ni(CN)_4^{2-} ion the individual deformation density of nickel is in qualitative agreement with that expected from crystal-field theory. As the repulsion from the electrons is much weaker perpendicular to the Ni(CN)_4^{2-} plane than within this plane, the deformation density is considerably larger in the perpendicular direction. However, the largest maxima in the individual deformation density around nickel are not found precisely in the planes defined by nickel and the four cyanide ligands or in the perpendicular direction just mentioned, which illustrates that it is necessary to consider the crystal field due to the whole crystalline environment.

Crystal structures of 2-Hydroxyimino-1-phenylethan-1-one and ethyl 3-Oxo-2-sodiooxyiminobutanoate

1978 ◽  
Vol 31 (4) ◽  
pp. 745 ◽  
Author(s):  
CL Raston ◽  
RP Sharma ◽  
BW Skelton ◽  
AH White
Keyword(s):  
Single Crystal ◽  
Least Squares ◽  
Crystal Structures ◽  
Sodium Ion ◽  
Water Molecules ◽  
Sodium Ions ◽  
X Ray Diffraction ◽  
X Ray

The crystal structures of the title compounds, PhCOCH=NOH (5) and Na+[MeCOC(=NO-)CO2Et],-2H2O (10), have been determined by single-crystal X-ray diffraction at 295 K and refined by least squares to R 0.051, 0.062 (815, 1199 'observed' reflections) respectively. Crystals of (5) are monoclinic, P21/n, a 14.177(6), b 5.075(4), c 11.049(6) Ǻ, β 112.89(3)°, Z4. Crystals of (10) are tetragonal, 141/a, a 19.41(1), c 10.643(5)Ǻ Z 16. In (5), within the C=NOH group, C-N is 1.263(4) and N-O is 1.375(4)Ǻ; in (10) C-N is 1.318(6) and N-O is 1.321(5)Ǻ. In (10), the (presumably) negative C=NO- group does not coordinate the sodium ion; the latter is bridged by water molecules, occupying four close coordination positions [2.405(4)-2.552(4)Ǻ] in an interesting bridged polymeric array while the remaining two coordination positions are occupied by two ligand C=O groups [2.363(4), 2.393(4) Ǻ], the ligands also bridging sodium ions.

Opening and Narrowing of the Water H—O—H Angle by Hydrogen-Bonding Effects: Re-inspection of Neutron Diffraction Data

1998 ◽  
Vol 54 (4) ◽  
pp. 464-470 ◽  
Author(s):  
T. Steiner
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Neutron Diffraction ◽  
Diffraction Data ◽  
Water Molecules ◽  
Hydroxyl Groups ◽  
Secondary Effects ◽  
X Ray Diffraction ◽  
X Ray ◽  
Sample Average

For 71 water molecules donating two Ow—H...O hydrogen bonds, the correlation of the covalent H—O—H angle and the O...Ow...O angle is inspected from 49 well refined organic and organometallic neutron diffraction crystal structures. Compared to sample average, the water angle is opened for large and narrowed for small O...Ow...O angles. Notably, the H—O—H angle is widened compared with the gas phase value even for small O...Ow...O. Related behavior is observed for chloride anion acceptors. The correlation exhibits a considerable scatter which should not be interpreted as experimental inaccuracies, but as secondary effects. Possible secondary effects are multi-center hydrogen bonding and effects of coordination to the water O atom. In a comparative test, low-temperature X-ray diffraction data were shown to be completely unsuitable for this type of analysis. The dependence of the C—O—H angle on the C—O...O angle in hydrogen bonds donated by hydroxyl groups in carbohydrates is also shown.

Charge Density in Orthorhombic NiSO4.7H2O at Room Temperature and 25 K

1997 ◽  
Vol 53 (3) ◽  
pp. 325-336 ◽  
Author(s):  
H. Ptasiewicz-Bak ◽  
I. Olovsson ◽  
G. J. McIntyre
Keyword(s):  
Charge Density ◽  
Lone Pair ◽  
Nickel Sulfate ◽  
Ligand Field ◽  
Water Molecules ◽  
Sulfate Heptahydrate ◽  
X Ray ◽  
Crystalline Environment ◽  
The Individual ◽  
Water Ligands

The charge-density distribution in the title compound nickel sulfate heptahydrate has been determined by multipole refinement against single-crystal X-ray intensity data. For the refinement at 25 K hydrogen positions and displacement parameters were fixed to values determined from neutron data. The charge density based on the deformation functions of all atoms in the structure is compared with the individual densities calculated from the deformation functions of only nickel or the separate water molecules. In this way the effects of simple superposition of the individual densities have been studied. The individual deformation density around nickel is in good qualitative agreement with that expected for an approximately octahedral Ni(H2O)6 2+ complex in a weak ligand field. However, the maximum densities are not found precisely in the planes defined by nickel and the six water ligands, which illustrates that it is necessary to consider the crystal field due to the whole crystalline environment. The individual densities of the water molecules show clear polarization of the lone-pair densities according to the coordination of the water molecules: tetrahedral coordination leads to two resolved lone-pair peaks, whereas planar trigonal coordination leads to just one single peak. Crystal data: NiSO4.7H2O, M r = 280.87, P212121, Z = 4. At T = 25 K: a = 6.706 (3), b = 11.796 (6), c = 11.949 (6) Å, V = 945 (1) Å3, D x = 1.977 Mg m−3. At 295 K: a = 6.751 (4), b = 11.746 (7), c = 12.003 (8) Å, V = 952 (1) Å3, D x = 1.959 Mg m−3. X-ray study: F(000) = 584, λ(Mo Kα) = 0.71069 Å, μ = 2.255 mm−1. At 25 K: R(F) = 0.014 for 10 185 reflections. At 295 K: R(F) = 0.015 for 5723 reflections. Neutron study at 25 K: λ = 1.215 Å, μ = 0.261 mm−1, R(F) = 0.034 for 1381 reflections.

Preparation of Silk Fibroin/Bacterial Cellulose Composite Films and their Mechanical Properties

2007 ◽  
Vol 342-343 ◽  
pp. 741-744 ◽  
Author(s):  
Rira Jung ◽  
Hyoung Joon Jin
Keyword(s):  
Mechanical Properties ◽  
Bacterial Cellulose ◽  
Silk Fibroin ◽  
Composite Films ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
X Ray ◽  
The Individual ◽  
Fibroin Solution ◽  
Cellulose Composite

We prepared composite films consisting of two biocompatible materials, bacterial cellulose and silk fibroin. Aqueous silk fibroin solution and bacterial cellulose excreted by Acetobacter xylinum were used to fabricate the composite films. It was verified by field emission scanning electron microscopy and X-ray diffraction that the two components were finely blended and that the silk fibroin was crystallized during the composition of the films. The silk fibroin penetrated well between the individual fibrils of the bacterial cellulose, while the water molecules inside the pellicular bacterial cellulose were evaporating. The composite films did not dissolve in water due to the crystallization of the silk fibroin in the composite films. We also observed the change in the mechanical properties of the composite films according to the water content. The composite films became more flexible and tougher when they were dipped in water, whereas they were very brittle in the dehydrated state.

The water molecules in CuSO 4 .5H 2 O

1962 ◽  
Vol 266 (1324) ◽  
pp. 95-108 ◽  
Keyword(s):  
Hydrogen Bonds ◽  
Neutron Diffraction ◽  
Single Crystals ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Neutron Data ◽  
X Ray ◽  
Atomic Nuclei ◽  
Different Temperatures ◽  
Molecular Rotations

Single crystals of fully hydrated copper sulphate have been studied by neutron diffraction and the measurements have been used to construct projections of the neutron-scattering density, due to the atomic nuclei, on the three crystallographic axial planes. These provide full details of the shape and environment of the water molecules and of the hydrogen bonds which link together the atoms in the structure, which was originally proposed by Beevers & Lipson as a result of X -ray diffraction work. It is found that the H—O—H angles for all the water molecules are within a degree or two of the tetrahedral value and the hydrogen bonds have to be bent by up to 26° in order to accommodate them. Corresponding measurements have been made at a series of five different temperatures between 20 and 90°C in order to test a suggestion that molecular rotations of the water molecules occurred before the onset of dehydration: the neutron data refute this suggestion.

scholarly journals Evaluation of models determined by neutron diffraction and proposed improvements to their validation and deposition

2018 ◽  
Vol 74 (8) ◽  
pp. 800-813 ◽  
Author(s):  
Dorothee Liebschner ◽  
Pavel V. Afonine ◽  
Nigel W. Moriarty ◽  
Paul Langan ◽  
Paul D. Adams
Keyword(s):  
Neutron Diffraction ◽  
Current Model ◽  
Data Bank ◽  
Water Molecules ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
X Ray ◽  
Manual Intervention ◽  
Data Files

The Protein Data Bank (PDB) contains a growing number of models that have been determined using neutron diffraction or a hybrid method that combines X-ray and neutron diffraction. The advantage of neutron diffraction experiments is that the positions of all atoms can be determined, including H atoms, which are hardly detectable by X-ray diffraction. This allows the determination of protonation states and the assignment of H atoms to water molecules. Because neutrons are scattered differently by hydrogen and its isotope deuterium, neutron diffraction in combination with H/D exchange can provide information on accessibility, dynamics and chemical lability. In this study, the deposited data, models and model-to-data fit for all PDB entries that used neutron diffraction as the source of experimental data have been analysed. In many cases, the reported R work and R free values were not reproducible. In such cases, the model and data files were analysed to identify the reasons for this mismatch. The issues responsible for the discrepancies are summarized and explained. The analysis unveiled limitations to the annotation, deposition and validation of models and data, and a lack of community-wide accepted standards for the description of neutron models and data, as well as deficiencies in current model refinement tools. Most of the issues identified concern the handling of H atoms. Since the primary use of neutron macromolecular crystallography is to locate and directly visualize H atoms, it is important to address these issues, so that the deposited neutron models allow the retrieval of the maximum amount of information with the smallest effort of manual intervention. A path forward to improving the annotation, validation and deposition of neutron models and hybrid X-ray and neutron models is suggested.

scholarly journals Anomalous hydrogen dynamics of the ice VII–VIII transition revealed by high-pressure neutron diffraction

2020 ◽  
Vol 117 (12) ◽  
pp. 6356-6361 ◽  
Author(s):  
Kazuki Komatsu ◽  
Stefan Klotz ◽  
Shinichi Machida ◽  
Asami Sano-Furukawa ◽  
Takanori Hattori ◽  
...  
Keyword(s):  
Neutron Diffraction ◽  
Translational Motion ◽  
Simultaneous Increase ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Oxygen Sublattice ◽  
X Ray ◽  
Slowing Down ◽  
Solid Phases ◽  
Two Phases

Above 2 GPa the phase diagram of water simplifies considerably and exhibits only two solid phases up to 60 GPa, ice VII and ice VIII. The two phases are related to each other by hydrogen ordering, with the oxygen sublattice being essentially the same. Here we present neutron diffraction data to 15 GPa which reveal that the rate of hydrogen ordering at the ice VII–VIII transition decreases strongly with pressure to reach timescales of minutes at 10 GPa. Surprisingly, the ordering process becomes more rapid again upon further compression. We show that such an unusual change in transition rate can be explained by a slowing down of the rotational dynamics of water molecules with a simultaneous increase of translational motion of hydrogen under pressure, as previously suspected. The observed cross-over in the hydrogen dynamics in ice is likely the origin of various hitherto unexplained anomalies of ice VII in the 10–15 GPa range reported by Raman spectroscopy, X-ray diffraction, and proton conductivity.

Charge density in NiCl2.4H2O at 295 and 30 K

1999 ◽  
Vol 55 (6) ◽  
pp. 830-840 ◽  
Author(s):  
H. Ptasiewicz-Bak ◽  
I. Olovsson ◽  
G. J. McIntyre
Keyword(s):  
Lone Pair ◽  
Chloride Ions ◽  
Water Molecules ◽  
Nickel Ion ◽  
X Ray ◽  
Charge Densities ◽  
Crystalline Environment ◽  
Coordinated Water ◽  
The Individual ◽  
Two Peaks

The charge distribution has been determined by multipole refinements against single-crystal X-ray diffraction data. In the refinements a comparison was made between the densities based on H-atom parameters from X-ray and neutron data, respectively. X-ray study: λ(Mo Kα) = 0.71073 Å, F(000) = 408; at 30 K: R(F) = 0.015 for 6686 reflections; at 295 K: R(F) = 0.022 for 4630 reflections. The nickel ion is octahedrally surrounded by four water molecules and two chloride ions, forming a locally neutral Ni(H2O)4Cl2 complex. Two of the water molecules are coordinated to nickel approximately in one of the tetrahedral (`lone-pair') directions; the other two are trigonally coordinated. At 30 K one H atom in one of the trigonally coordinated water molecules is disordered, with equal occupation of two different positions. Owing to the polarizing influence of the nickel ion there are two peaks in the lone-pair plane of the water molecules when these are tetrahedrally coordinated; for those trigonally coordinated there is just one peak. The individual (`partial') charge densities, calculated from the deformation functions of only nickel or the separate water molecules, have also been calculated to study the effects of superposition of the individual densities. In the individual density of nickel an excess is observed in the diagonal directions and a deficiency in the ligand directions. However, owing to the influence of the whole crystalline environment, the maxima around nickel are not found in the planes defined by nickel and the six ligands.

Texture measurements in Al2O3 using BEKP

1994 ◽  
Vol 52 ◽  
pp. 608-609
Author(s):  
M. D. Vaudin ◽  
J. P. Cline
Keyword(s):  
Neutron Diffraction ◽  
Rapid Method ◽  
Crystallographic Orientation ◽  
Specimen Surface ◽  
X Ray Diffraction ◽  
Anisotropic Crystal ◽  
X Ray ◽  
Verification Method ◽  
Crystal Properties ◽  
Backscattered Electron

The study of preferred crystallographic orientation (texture) in ceramics is assuming greater importance as their anisotropic crystal properties are being used to advantage in an increasing number of applications. The quantification of texture by a reliable and rapid method is required. Analysis of backscattered electron Kikuchi patterns (BEKPs) can be used to provide the crystallographic orientation of as many grains as time and resources allow. The technique is relatively slow, particularly for noncubic materials, but the data are more accurate than any comparable technique when a sufficient number of grains are analyzed. Thus, BEKP is well-suited as a verification method for data obtained in faster ways, such as x-ray or neutron diffraction. We have compared texture data obtained using BEKP, x-ray diffraction and neutron diffraction. Alumina specimens displaying differing levels of axisymmetric (0001) texture normal to the specimen surface were investigated.BEKP patterns were obtained from about a hundred grains selected at random in each specimen.

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